My comments are interspersed -- including your requested "paragraph" at the bottom.
On Jan 26, 2004, at 5:06 AM, Miguel Howard wrote:
I am discouraged/concerned to hear that the behavior on Camino/Mozilla is
different. It looks like they are mapping the right button to the
middle-button ... I hope that the mouse event behavior on Camino/Mozilla
is not different from Safari ...
By mouse event, you mean??
This can be easily done.Wish: I would like to see a "heteroatom" choice in the selection contextual menu. That would allow the user to select any atoms (like metals) that are not part of the list. That can be done in the scripting, but I would like to be able to do it as a user.
Is there a *short* list of other things?
From the simple to the complex. I think that if we are dealing with biomolecules, phosphorous (P) ought to be selectable.
Then an entry for heteroatoms which would get anything else. Thus, you could pick out metal ions complexed in the structure of a protein, for example.
And then, what about an atom number popup in which you could enter a specific atom number to select. That would give the user great flexibility.
I would love to see ligand groups as well. That is harder, I think. For example, in hemoglobin, you could select the heme group for highlighting. I think it is possible in both Rasmol and Chime.
Question: I have played with the "move" script and have figured out what most of the spaces are for. But what are the 7th and 8th for? Can't seem to make them do anything.
The 7th and 8th parameters to 'move' are ignored. The spots are maintained
for backward compatibility with existing scripts.
The 7th parameter is for translation in the z dimension. It is essentially
the same as saying:
translate z 25
which also does ... absolutely nothing.
The 8th parameter is for a minimum frame rate. But I thought it was a bad
idea. Jmol does the best frame-rate that it can, up to 30 frames/second,
but will *always* hit time time target.
move {x-rotation} {y-rotation} {z-rotation} {zoom-factor} {x-translation}
{y-translation} {z-translation IGNORED} {frame-rate IGNORED} {time}
Thanks. That is basically what I discovered empirically.
My latest venture is displayed at : http://www.saintmarys.edu/~pbays/Complexes/Complexes.htm. Obviously, we are doing some meta- ligand chemistry in my intro course :)
Looks great!
I am going to try to drag you into the 'colors' discussion ... What color
do you think that Magnesium should be?
Not sure. Isn't there some sort of standardized cpk coloring?
If you can, please send me 1 paragraph (no more!) that tells me about the
interesting 'bonding' of ferrocene :-)
Since I understand that you are not a chemist, I will do this simply -- so the inorganicers on the list should not jump on me:)
Ferrocene can be thought of as being made from iron II and 2 cyclopentadienyl anions. To think of cyclopentadiene, think about a five-membered ring with two double bonds in it. Now if you remove a hydrogen from the carbon which is not double-bonded, you get an anion. This negatively charged system now has 6 pi electrons and behaves like benzene. Sometimes you will see benzene with three double bonds; other times with a circle in the ring to emphasize that it is aromatic. Likewise with the cyclopentadienyl anion. Now the question: is the iron coordinated with each carbon of a ring as the left image shows, or to the pi system and the right structure shows, using a pseudoatom in the middle of the ring as the bonding site? The left image was downloaded from someone's web site as a pdb file. The right, I made myself using Spartan and exporting as a pdb file.
Hope that paragraph helps and is not too long :)
Phil
J. Philip Bays Department of Chemistry and Physics Saint Mary's College Notre Dame IN 46556 [EMAIL PROTECTED]
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